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Links from GEO DataSets

Items: 20

1.

The SAGA coactivator regulates the expression of nearly all genes transcribed by RNA polymerase II

(Submitter supplied) The SAGA coactivator complex facilitates transcription initiation through chromatin-modifying activities and interaction with TBP. SAGA was suggested to regulate the expression of about 10% of yeast genes, leading to the longstanding distinction of SAGA-dominated from TFIID-dominated genes, depending on the complex used to recruit TBP to promoters. We reassessed the genome-wide localization of SAGA by using ChEC-seq and its role on transcription through quantification of newly-synthesized mRNA. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17342
5 Samples
Download data: RTF, WIG
Series
Accession:
GSE97379
ID:
200097379
2.

SAGA Is a General Cofactor for RNA Polymerase II Transcription

(Submitter supplied) The SAGA co-activator has been implicated in the regulation of a smal subset of genes in budding yeast in transcriptomic analyses performed in steady-state levels of RNA. We used microarrays to analyse newly-synthesized RNA in several mutants for the SAGA complex to disclose and readdress the impact of this complex in RNA Polymerase II transcription.
Organism:
Schizosaccharomyces pombe; Saccharomyces cerevisiae
Type:
Expression profiling by array
Platform:
GPL2529
68 Samples
Download data: CEL
Series
Accession:
GSE96849
ID:
200096849
3.

Transcription of nearly all yeast RNA Polymerase II-transcribed genes is dependent on transcription factor TFIID

(Submitter supplied) Previous studies suggested that expression of most yeast mRNAs is dominated by either transcription factor TFIID or SAGA. We reexamined this longstanding problem by rapid depletion of TFIID subunits and measurement of changes in nascent transcription. We find that transcription of nearly all mRNAs is strongly dependent on TFIID function. Degron-dependent depletion of Tafs 1,2,7,11, and 13 showed similar transcription decreases for genes in the Taf1-depleted, Taf1-enriched, TATA-containing and TATA-less gene classes. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL17342
50 Samples
Download data: WIG
Series
Accession:
GSE97081
ID:
200097081
4.

Transcription of Nearly All Yeast RNA Polymerase II-Transcribed Genes Is Dependent on Transcription Factor TFIID

(Submitter supplied) RNA Pol II transcription has been implied to be either regulated by the general transcription factor TFIID or the co-activator SAGA. Also, this dominancy of either SAGA or TFIID might be according to the existance, or not, of a TATA consensus sequence. We used microarrays to analyse newly-synthesized RNA in two mutants that allow conditional nuclear depletion of Taf4 or Taf5 to reevaluate whether some genes are more affected than others.
Organism:
Schizosaccharomyces pombe; Saccharomyces cerevisiae
Type:
Expression profiling by array
Platform:
GPL2529
16 Samples
Download data: CEL
Series
Accession:
GSE96830
ID:
200096830
5.

Two separate roles for the transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA [ChIP-Seq]

(Submitter supplied) Deletions within genes coding for subunits of the transcription coactivator SAGA caused strong genome-wide defects in transcription and SAGA-mediated chromatin modifications. In contrast, rapid SAGA depletion produced only modest transcription defects at 13% of protein-coding genes – genes that are generally more sensitive to rapid TFIID depletion. However, transcription of these “coactivator-redundant” genes is strongly affected by rapid depletion of both factors, showing the overlapping functions of TFIID and SAGA at this gene set. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17342
32 Samples
Download data: WIG
Series
Accession:
GSE142183
ID:
200142183
6.

Two separate roles for the transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA [RNA-Seq]

(Submitter supplied) Deletions within genes coding for subunits of the transcription coactivator SAGA caused strong genome-wide defects in transcription and SAGA-mediated chromatin modifications. In contrast, rapid SAGA depletion produced only modest transcription defects at 13% of protein-coding genes – genes that are generally more sensitive to rapid TFIID depletion. However, transcription of these “coactivator-redundant” genes is strongly affected by rapid depletion of both factors, showing the overlapping functions of TFIID and SAGA at this gene set. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17342
11 Samples
Download data: CSV
Series
Accession:
GSE142182
ID:
200142182
7.

Two separate roles for the transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17342
128 Samples
Download data: CSV, WIG
Series
Accession:
GSE142122
ID:
200142122
8.

Two separate roles for the transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA [ChEC-Seq]

(Submitter supplied) Deletions within genes coding for subunits of the transcription coactivator SAGA caused strong genome-wide defects in transcription and SAGA-mediated chromatin modifications. In contrast, rapid SAGA depletion produced only modest transcription defects at 13% of protein-coding genes – genes that are generally more sensitive to rapid TFIID depletion. However, transcription of these “coactivator-redundant” genes is strongly affected by rapid depletion of both factors, showing the overlapping functions of TFIID and SAGA at this gene set. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17342
25 Samples
Download data: WIG
Series
Accession:
GSE142120
ID:
200142120
9.

Two separate roles for the transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA [RNA]

(Submitter supplied) Deletions within genes coding for subunits of the transcription coactivator SAGA caused strong genome-wide defects in transcription and SAGA-mediated chromatin modifications. In contrast, rapid SAGA depletion produced only modest transcription defects at 13% of protein-coding genes – genes that are generally more sensitive to rapid TFIID depletion. However, transcription of these “coactivator-redundant” genes is strongly affected by rapid depletion of both factors, showing the overlapping functions of TFIID and SAGA at this gene set. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17342
60 Samples
Download data: CSV
Series
Accession:
GSE133004
ID:
200133004
10.

Effect of loss of function of Gal11/Med15 and Med3 from the Mediator tail module in budding yeast

(Submitter supplied) Gene expression was compared for wild type yeast (BY4741) and yeast lacking Gal11/Med15 and Med3, or from a gal11-myc med3∆ strain. The gal11-myc allele shows a partial loss of function when combined with med3∆. Expression was analyzed for yeast grown in YPD as well as in CSM. We also examined gene expression of the wild type strain BY4742 grown in YPD and include that data here.
Organism:
Saccharomyces cerevisiae; Schizosaccharomyces pombe
Type:
Expression profiling by array
Platform:
GPL2529
21 Samples
Download data: CEL, TXT
Series
Accession:
GSE31774
ID:
200031774
11.

Evolutionarily conserved C-terminal region of TAF9 is critical for SAGA and TFIID recruitment to promoters and transcriptional activation

(Submitter supplied) TFIID and SAGA complexes play a critical role in RNA Polymerase II dependent activated transcription. Although the two regulatory complexes are recruited to promoters by activation domain-interactions, the contribution of the different subunits or the different domains of the individual subunits is not completely understood. Taf9 is a shared subunit in TFIID and SAGA and has an N-terminal H3-like histone fold domain and a highly conserved C-terminal domain, Taf9-CTD. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by array
Platform:
GPL14009
14 Samples
Download data: TXT
Series
Accession:
GSE44544
ID:
200044544
12.

The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. The SAGA co-activator complex contains distinct chromatin-modifying activities and is recruited by DNA-bound activators to regulate the expression of a subset of genes. Surprisingly, recent studies revealed little overlap between genome-wide SAGA-binding profiles and changes in gene expression upon depletion of subunits of the complex. As indicators of SAGA recruitment on chromatin, we monitored in yeast and human cells the genome-wide distribution of histone H3K9 acetylation and H2B ubiquitination, which are respectively deposited or removed by SAGA. more...
Organism:
Saccharomyces cerevisiae; Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL11154 GPL10999 GPL13821
23 Samples
Download data: WIG
Series
Accession:
GSE59370
ID:
200059370
13.

The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription [Yeast cells]

(Submitter supplied) The SAGA co-activator complex contains distinct chromatin-modifying activities and is recruited by DNA-bound activators to regulate the expression of a subset of genes. Surprisingly, recent studies revealed little overlap between genome-wide SAGA-binding profiles and changes in gene expression upon depletion of subunits of the complex. As indicators of SAGA recruitment on chromatin, we monitored in yeast and human cells the genome-wide distribution of histone H3K9 acetylation and H2B ubiquitination, which are respectively deposited or removed by SAGA. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13821
19 Samples
Download data: WIG
Series
Accession:
GSE52997
ID:
200052997
14.

The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription [HeLa cells]

(Submitter supplied) The SAGA co-activator complex contains distinct chromatin-modifying activities and is recruited by DNA-bound activators to regulate the expression of a subset of genes. Surprisingly, recent studies revealed little overlap between genome-wide SAGA-binding profiles and changes in gene expression upon depletion of subunits of the complex. As indicators of SAGA recruitment on chromatin, we monitored in yeast and human cells the genome-wide distribution of histone H3K9 acetylation and H2B ubiquitination, which are respectively deposited or removed by SAGA. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL11154 GPL10999
4 Samples
Download data: WIG
Series
Accession:
GSE52860
ID:
200052860
15.

The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally

(Submitter supplied) Eukaryotic transcription is regulated through two complexes, the general transcription factor IID (TFIID) and the coactivator Spt-Ada-Gcn5 acetyltransferase (SAGA). Recent findings confirm that both TFIID and SAGA contribute to the synthesis of nearly all transcripts and are recruited genome-wide in yeast. However, how this broad recruitment confers selectivity under specific conditions remains an open question. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL19756 GPL13821
22 Samples
Download data: NARROWPEAK
Series
Accession:
GSE65902
ID:
200065902
16.

Genomic Run On (GRO): determination of the nascent transcriptional rates and mRNA levels in several yeast mutants (SAC3, SUS1, SRC1)

(Submitter supplied) We analyzed the effect of SAC3, SUS1 and SRC1 on the transcription rates, mRNA stabilities and mRNA levels by doing GRO experiments in a deletion mutants and the partial C-truncated version of Sac3 comparing with a wild type. Some data for mRNA amounts (sus1 ans src1 mutants) are not included because were already in GEO database: GSE920 and GSE6370 accession numbers.
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by array
Platforms:
GPL4565 GPL8568
9 Samples
Download data: TXT
Series
Accession:
GSE63769
ID:
200063769
17.

GS003: Tight cooperation between Mot1p and NC2β in regulating genome-wide transcription, repression of transcription following heat shock induction and genetic interaction with SAGA.

(Submitter supplied) TATA-binding protein (TBP) is central to the regulation of transcription initiation. Recruitment of TBP to target genes can be positively regulated by one of two basal transcription factor complexes: SAGA or TFIID. Negative regulation of TBP promoter association can be performed by Mot1 or the NC2 complex. Recent evidence suggest that Mot1, NC2, and TBP form a DNA-dependent protein complex. Here, we compare the functions of Mot1 and NC2beta during basal and activated transcription using the anchor-away technique for conditional nuclear depletion. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by array
Platform:
GPL11232
12 Samples
Download data: TXT
Series
Accession:
GSE30148
ID:
200030148
18.

Supt3 mutant nascent RNA-seq

(Submitter supplied) Coactivator complexes regulate chromatin accessibility and transcription. SAGA (Spt-Ada-Gcn5 Acetyltransferase) is an evolutionary conserved coactivator complex. The core module scaffolds the entire SAGA complex and adopts a histone octamer-like structure, which consists of six histone fold domain (HFD)-containing proteins forming three histone fold (HF) pairs, to which the double HFD-containing SUPT3H adds an HF pair. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21103
4 Samples
Download data: TSV, TXT
Series
Accession:
GSE202823
ID:
200202823
19.

SUPT3H-less SAGA coactivator can assemble and function without significantly perturbing RNA polymerase II transcription in mammalian cells

(Submitter supplied) To analyse the genome-wide impact of inactivation of the Supt3h subunit of the SAGA complex on RNA polymerase II (Pol II) transcription in human U2OS cells and mouse embryonic stem cells (mESCs), we analysed newly synthesized RNA using 4sU-labelling in mutant and wildtype conditions.
Organism:
Homo sapiens; Mus musculus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL20301 GPL21103
8 Samples
Download data: TSV, TXT
Series
Accession:
GSE175901
ID:
200175901
20.

An integrated SAGA and TFIID PIC assembly pathway selective for poised and induced promoters

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19756
294 Samples
Download data: BW
Series
Accession:
GSE212655
ID:
200212655
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